Learning Unix/Linux
Click to add text
Bioinformatics Orientation 2008 Eric Bishop
Introduction: What is Unix?
An operating system Developed at AT&T Bell Labs in the 1960s Command Line Interpreter GUIs (Window systems) are now available
Introduction: Unix vs. Linux
Unix was the predecessor of Linux Linux is a variant of Unix
So
is Mac OS X, so much of this tutorial applies to Macs as well
Linux is open source Most of the machines youll use in the Bioinformatics program are running the Linux OS
Introduction: Why Unix/Linux?
Linux
is free Its fully customizable Its stable (i.e. it almost never crashes)
These
characteristics make it an ideal OS for programmers and scientists
Connecting to a Unix/Linux system
Open up a terminal:
Connecting to a Unix/Linux system
Open up a terminal:
The prompt
The current directory (path)
The host
What exactly is a shell?
After logging in, Linux/Unix starts another program called the shell The shell interprets commands the user types and manages their execution
The shell communicates with the internal part of the operating system called the kernel The most popular shells are: tcsh, csh, korn, and bash The differences are most times subtle For this tutorial, we are using bash
Shell commands are CASE SENSITIVE!
Help!
Whenever you need help with a command type man and the command name
Help!
Help!
Help!
Unix/Linux File System
NOTE: Unix file names are CASE SENSITIVE!
/home/mary/
/home/john/portfolio/
The Path
Command: pwd
To find your current path use pwd
Command: cd
To change to a specific directory use cd
Command: cd
~ is the location of your home directory
Command: cd
.. is the location of the directory below current one
Command: ls
To list the files in the current directory use ls
Command: ls
ls has many options
-l long list (displays lots of info) -t sort by modification time -S sort by size -h list file sizes in human readable format -r reverse the order
man ls for more options Options can be combined: ls -ltr
Command: ls -ltr
List files by time in reverse order with long listing
General Syntax: *
* can be used as a wildcard in unix/linux
Command: mkdir
To create a new directory use mkdir
Command: rmdir
To remove and empty directory use rmdir
Creating files in Unix/Linux
Requires the use of an Editor Various Editors:
1)
2) 3)
nano / pico vi emacs
Editing a file using pico or nano
Type pico or nano at the prompt
Editing a file using pico
To save use ctrl-x
Displaying a file
Various ways to display a file in Unix
cat less head tail
Command: cat
Dumps an entire file to standard output Good for displaying short, simple files
Command: less
less displays a file, allowing forward/backward movement within it
return
scrolls forward one line, space one page y scrolls back one line, b one page
use / to search for a string Press q to quit
Command: head
head displays the top part of a file By default it shows the first 10 lines -n option allows you to change that head -n50 file.txt displays the first 50 lines of file.txt
Command: head
Heres an example of using head:
Command: tail
Same as head, but shows the last lines
File Commands
Copying a file: cp Move or rename a file: mv Remove a file: rm
Command: cp
To copy a file use cp
Command: mv
To move a file to a different location use mv
Command: mv
mv can also be used to rename a file
Command: rm
To remove a file use rm
Command: rm
To remove a file recursively: rm r Used to remove all files and directories Be very careful, deletions are permanent in Unix/Linux
File permissions
Each file in Unix/Linux has an associated permission level This allows the user to prevent others from reading/writing/executing their files or directories Use ls -l filename to find the permission level of that file
Permission levels
r means read only permission w means write permission x means execute permission
In
case of directory, x grants permission to list directory contents
File Permissions
User (you)
File Permissions
Group
File Permissions
The World
Command: chmod
If you own the file, you can change its permissions with chmod Syntax: chmod [user/group/others/all]+[permission] [file(s)]
Below we grant execute permission to all:
Running a program (a.k.a. a job)
Make sure the program has executable permissions Use ./ to run the program
Running a program: an example
Running the sample perl script hello_world.pl
Ending a program
To end a program use ctrl-c. To try it:
Command: ps
To view the processes that youre running:
Command: top
To view the CPU usage of all processes:
Command: kill
To terminate a process use kill
Input/Output Redirection (piping)
Programs can output to other programs Called piping program_a | program_b
program_as output becomes program_bs input
program_a > file.txt
program_as output is written to a file called file.txt
program_a gets its input from a file called input.txt
program_a < input.txt
A few examples of piping
A few examples of piping
Command: wc
To count the characters, words, and lines in a file use wc The first column in the output is lines, the second is words, and the last is characters
A few examples of piping
Command: grep
To search files in a directory for a specific string use grep
Command: diff
To compare to files for differences use diff
Try:
diff /dev/null hello.txt /dev/null is a special address -- it is always empty, and anything moved there is deleted
ssh, scp
ssh is used to securely log in to remote systems, successor to telnet ssh [username]@[hostname] Try: ssh yourusername@localhost Type exit to log out of session
Scp is used to copy files to/from remote systems, syntax is similar to cp:
scp [local path] [usernme]@[hostname]:[remote file path]
Try:
scp hello.txt yourusername@localhost:scp-test.txt
Unix Web Resources
http://www.ee.surrey.ac.uk/Teaching/Unix/
http://www.ugu.com/sui/ugu/show?help.be ginners
http://en.wikipedia.org/wiki/Unix
